YRC Public Data Repository - Protein Structure Prediction

Protein:	gi\|30062653, gi\|...
Organism:	Shigella flexneri 2a str. 2457T
Length:	273 amino acids
Reference:	Drew K, et al. (2011) The proteome folding project: Proteome-scale prediction of structure and function. Genome Res. 2011 Sep 16

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Top Sequence Alignment Hits

Listed below are up to the top 10 sequence alignment matches, by species, for the PSI-BLAST search against the protein sequence for gi|30062653, gi|....

Description	E-value	Query Range	Subject Range
gi\|253773856, gi... - gi\|254288035\|ref\|YP_003053783.1\| NAD-dependent deacetylase [Escherichia coli BL21(DE3)], gi\|25397734... gi\|16129083\|ref\|... - NAD-dependent deacetylase [Escherichia coli K12], deacetylase of acetyl-CoA synthetase, NAD-dependen... gi\|83584887, gi\|... - gi\|83584887\|ref\|ZP_00923545.1\| COG0846: NAD-dependent protein deacetylases, SIR2 family [Escherichia... gi\|251784650, gi... - gi\|251784650\|ref\|YP_002998954.1\| hypothetical protein B21_01126 [Escherichia coli BL21], gi\|24237692... gi\|4062692, gi\|8... - gi\|89107966\|ref\|AP_001746.1\| deacetylase of acetyl-CoA synthetase, NAD-dependent [Escherichia coli s... gi\|238860741, gi... - gi\|238900374\|ref\|YP_002926170.1\| deacetylase of acetyl-CoA synthetase, NAD-dependent [Escherichia co... gi\|75511391, gi\|... - gi\|75511391\|ref\|ZP_00734074.1\| COG0846: NAD-dependent protein deacetylases, SIR2 family [Escherichia... gi\|4062692, gi\|1... - gi\|4062692\|dbj\|BAA35940.1\| deacetylase of acetyl-CoA synthetase, NAD-dependent [Escherichia coli W31... gi\|124499575, gi... - gi\|124529867\|ref\|ZP_01700711.1\| Silent information regulator protein Sir2 [Escherichia coli B], gi\|1... gi\|169755413, gi... - gi\|170020485\|ref\|YP_001725439.1\| NAD-dependent deacetylase [Escherichia coli ATCC 8739], gi\|16975541... gi\|170080771, gi... - gi\|170080771\|ref\|YP_001730091.1\| deacetylase of acetyl-CoA synthetase, NAD-dependent [Escherichia co... gi\|157160646, gi... - gi\|75195303\|ref\|ZP_00705373.1\| COG0846: NAD-dependent protein deacetylases, SIR2 family [Escherichia... NPD_ECOLI - NAD-dependent deacetylase (EC 3.5.1.-) (Regulatory protein SIR2 homolog) - Escherichia coli gi\|256023182\|ref... - NAD-dependent deacetylase [Escherichia sp. 4_1_40B] gi\|254161227, gi... - gi\|254161227\|ref\|YP_003044335.1\| NAD-dependent deacetylase [Escherichia coli B str. REL606], gi\|2539...	316.0	[0..1]	[273..1]
gi\|75239618, gi\|... - gi\|75239618\|ref\|ZP_00723585.1\| COG0846: NAD-dependent protein deacetylases, SIR2 family [Escherichia... gi\|115512429, gi... - gi\|117623305\|ref\|YP_852218.1\| NAD-dependent deacetylase [Escherichia coli APEC O1], gi\|115512429\|gb\|... gi\|215264403, gi... - gi\|215486331\|ref\|YP_002328762.1\| NAD-dependent deacetylase [Escherichia coli O127:H6 str. E2348/69],... gi\|218689072, gi... - gi\|218689072\|ref\|YP_002397284.1\| NAD-dependent deacetylase [Escherichia coli ED1a], gi\|218426636\|emb... gi\|218364770, gi... - gi\|218558001\|ref\|YP_002390914.1\| NAD-dependent deacetylase [Escherichia coli S88], gi\|218364770\|emb\|... NPD_ECOL6 - NAD-dependent deacetylase OS=Escherichia coli O6 GN=cobB PE=3 SV=1 gi\|227886523, gi... - gi\|227886523\|ref\|ZP_04004328.1\| NAD-dependent deacetylase [Escherichia coli 83972], gi\|227836727\|gb\|... gi\|110641296, gi... - gi\|110641296\|ref\|YP_669026.1\| NAD-dependent deacetylase [Escherichia coli 536], gi\|110342888\|gb\|ABG6... gi\|237706894, gi... - gi\|237706894\|ref\|ZP_04537375.1\| NAD-dependent deacetylase [Escherichia sp. 3_2_53FAA], gi\|226898104\|... gi\|91071849, gi\|... - gi\|91210275\|ref\|YP_540261.1\| NAD-dependent deacetylase [Escherichia coli UTI89], gi\|91071849\|gb\|ABE0... gi\|26247264, gi\|... - gi\|26247264\|ref\|NP_753304.1\| NAD-dependent deacetylase [Escherichia coli CFT073], gi\|26107665\|gb\|AAN...	316.0	[0..1]	[273..1]
gi\|12514670, gi\|... - gi\|15801237\|ref\|NP_287254.1\| NAD-dependent deacetylase [Escherichia coli O157:H7 EDL933], gi\|1251467... gi\|260854603\|ref... - deacetylase of acetyl-CoA synthetase, NAD-dependent [Escherichia coli O26:H11 str. 11368] gi\|209772938, gi... - pir\|\|F85675 hypothetical protein cobB [imported] - Escherichia coli (strain O157:H7, substrain EDL9... gi\|293414413\|ref... - NAD-dependent deacetylase [Escherichia coli B185] gi\|261226976\|ref... - NAD-dependent deacetylase [Escherichia coli O157:H7 str. FRIK2000] gi\|291282140\|ref... - NAD-dependent deacetylase [Escherichia coli O55:H7 str. CB9615] gi\|13360962, gi\|... - gi\|15830752\|ref\|NP_309525.1\| NAD-dependent deacetylase [Escherichia coli O157:H7 str. Sakai], gi\|133... gi\|256018624\|ref... - NAD-dependent deacetylase [Shigella sp. D9] gi\|168757835, gi... - gi\|189355231\|gb\|EDU73650.1\| NAD-dependent deacetylase [Escherichia coli O157:H7 str. EC4401], gi\|168... gi\|254792503, gi... - gi\|254792503\|ref\|YP_003077340.1\| deacetylase of acetyl-CoA synthetase, NAD-dependent [Escherichia co... gi\|188014637, gi... - gi\|188014637\|gb\|EDU52759.1\| NAD-dependent deacetylase [Escherichia coli O157:H7 str. EC4113], gi\|168... gi\|189359873, gi... - gi\|189359873\|gb\|EDU78292.1\| NAD-dependent deacetylase [Escherichia coli O157:H7 str. EC4486], gi\|168... gi\|189365429, gi... - gi\|189365429\|gb\|EDU83845.1\| NAD-dependent deacetylase [Escherichia coli O157:H7 str. EC4501], gi\|168... gi\|260843360\|ref... - deacetylase of acetyl-CoA synthetase, NAD-dependent [Escherichia coli O103:H2 str. 12009] gi\|168783490, gi... - gi\|188999150\|gb\|EDU68136.1\| NAD-dependent deacetylase [Escherichia coli O157:H7 str. EC4076], gi\|168... gi\|187767858, gi... - gi\|187767858\|gb\|EDU31702.1\| NAD-dependent deacetylase [Escherichia coli O157:H7 str. EC4196], gi\|168... gi\|189377225, gi... - gi\|189377225\|gb\|EDU95641.1\| NAD-dependent deacetylase [Escherichia coli O157:H7 str. EC508], gi\|1688... gi\|293409486\|ref... - conserved hypothetical protein [Escherichia coli B354] gi\|189370394, gi... - gi\|189370394\|gb\|EDU88810.1\| NAD-dependent deacetylase [Escherichia coli O157:H7 str. EC869], gi\|1687... gi\|82544412, gi\|... - gi\|82544412\|ref\|YP_408359.1\| NAD-dependent deacetylase [Shigella boydii Sb227], gi\|81245823\|gb\|ABB66... NPD_ECO57 - NAD-dependent deacetylase OS=Escherichia coli O157:H7 GN=cobB PE=3 SV=1 gi\|75190177 - gi\|75190177\|ref\|ZP_00703444.1\| COG0846: NAD-dependent protein deacetylases, SIR2 family [Escherichia... gi\|218351385, gi... - gi\|218694653\|ref\|YP_002402320.1\| NAD-dependent deacetylase [Escherichia coli 55989], gi\|218351385\|em... gi\|75208953, gi\|... - gi\|75208953\|ref\|ZP_00709223.1\| COG0846: NAD-dependent protein deacetylases, SIR2 family [Escherichia... gi\|218553697, gi... - gi\|218553697\|ref\|YP_002386610.1\| NAD-dependent deacetylase [Escherichia coli IAI1], gi\|218360465\|emb... gi\|194418119, gi... - gi\|83569557\|ref\|ZP_00921009.1\| COG0846: NAD-dependent protein deacetylases, SIR2 family [Shigella dy... gi\|218370364, gi... - gi\|218700378\|ref\|YP_002408007.1\| NAD-dependent deacetylase [Escherichia coli IAI39], gi\|218370364\|em... gi\|193066282, gi... - gi\|75255635\|ref\|ZP_00727414.1\| COG0846: NAD-dependent protein deacetylases, SIR2 family [Escherichia... gi\|73855158, gi\|... - gi\|74311681\|ref\|YP_310100.1\| NAD-dependent deacetylase [Shigella sonnei Ss046], gi\|73855158\|gb\|AAZ87... gi\|190901381, gi... - gi\|75228209\|ref\|ZP_00714868.1\| COG0846: NAD-dependent protein deacetylases, SIR2 family [Escherichia... gi\|261256210\|ref... - NAD-dependent deacetylase [Escherichia coli O157:H7 str. FRIK966] gi\|75234229, gi\|... - gi\|75234229\|ref\|ZP_00718622.1\| COG0846: NAD-dependent protein deacetylases, SIR2 family [Escherichia... gi\|195938879 - gi\|195938879\|ref\|ZP_03084261.1\| NAD-dependent deacetylase [Escherichia coli O157:H7 str. EC4024] gi\|170683527, gi... - gi\|170683527\|ref\|YP_001744058.1\| NAD-dependent deacetylase [Escherichia coli SMS-3-5], gi\|170521245\|... gi\|208731481, gi... - gi\|208814833\|ref\|ZP_03256012.1\| NAD-dependent deacetylase [Escherichia coli O157:H7 str. EC4045], gi... gi\|208728860, gi... - gi\|208809059\|ref\|ZP_03251396.1\| NAD-dependent deacetylase [Escherichia coli O157:H7 str. EC4206], gi... gi\|209397898, gi... - gi\|209397898\|ref\|YP_002269965.1\| NAD-dependent deacetylase [Escherichia coli O157:H7 str. EC4115], g... gi\|208737689, gi... - gi\|208822204\|ref\|ZP_03262523.1\| NAD-dependent deacetylase [Escherichia coli O157:H7 str. EC4042], gi... gi\|217318505, gi... - gi\|217328078\|ref\|ZP_03444160.1\| NAD-dependent deacetylase [Escherichia coli O157:H7 str. TW14588], g... gi\|209918376, gi... - gi\|209918376\|ref\|YP_002292460.1\| NAD-dependent deacetylase [Escherichia coli SE11], gi\|209911635\|dbj... gi\|260867482\|ref... - deacetylase of acetyl-CoA synthetase, NAD-dependent [Escherichia coli O111:H- str. 11128]	315.0	[0..1]	[273..1]
gi\|205329698, gi... - gi\|205329698\|gb\|EDZ16462.1\| NAD-dependent deacetylase [Salmonella enterica subsp. enterica serovar 4... gi\|161614548, gi... - gi\|161614548\|ref\|YP_001588513.1\| NAD-dependent deacetylase [Salmonella enterica subsp. enterica sero... gi\|161501944 - gi\|161501944\|ref\|NP_455713.2\| NAD-dependent deacetylase [Salmonella enterica subsp. enterica serovar... gi\|161486798 - gi\|161486798\|ref\|NP_805475.2\| NAD-dependent deacetylase [Salmonella enterica subsp. enterica serovar... gi\|205347302, gi... - gi\|205347302\|gb\|EDZ33933.1\| NAD-dependent deacetylase [Salmonella enterica subsp. enterica serovar H... gi\|205336686, gi... - gi\|205336686\|gb\|EDZ23450.1\| NAD-dependent deacetylase [Salmonella enterica subsp. enterica serovar H... gi\|197288105, gi... - gi\|197288105\|gb\|EDY27492.1\| NAD-dependent deacetylase [Salmonella enterica subsp. enterica serovar S... gi\|168233101, gi... - gi\|205332645\|gb\|EDZ19409.1\| NAD-dependent deacetylase [Salmonella enterica subsp. enterica serovar K... gi\|206709075, gi... - gi\|207857272\|ref\|YP_002243923.1\| NAD-dependent deacetylase [Salmonella enterica subsp. enterica sero... gi\|205272826, gi... - gi\|205353045\|ref\|YP_002226846.1\| NAD-dependent deacetylase [Salmonella enterica subsp. enterica sero... gi\|204320229, gi... - gi\|204930770\|ref\|ZP_03221643.1\| NAD-dependent deacetylase [Salmonella enterica subsp. enterica serov... gi\|199602032, gi... - gi\|200389587\|ref\|ZP_03216198.1\| NAD-dependent deacetylase [Salmonella enterica subsp. enterica serov... gi\|213649276 - gi\|213649276\|ref\|ZP_03379329.1\| NAD-dependent deacetylase [Salmonella enterica subsp. enterica serov... gi\|213609841 - gi\|213609841\|ref\|ZP_03369667.1\| NAD-dependent deacetylase [Salmonella enterica subsp. enterica serov... gi\|213425044 - gi\|213425044\|ref\|ZP_03357794.1\| NAD-dependent deacetylase [Salmonella enterica subsp. enterica serov... gi\|213051990 - gi\|213051990\|ref\|ZP_03344868.1\| NAD-dependent deacetylase [Salmonella enterica subsp. enterica serov... gi\|194469556, gi... - gi\|194469556\|ref\|ZP_03075540.1\| NAD-dependent deacetylase [Salmonella enterica subsp. enterica serov... gi\|194449568, gi... - gi\|194449568\|ref\|YP_002045221.1\| NAD-dependent deacetylase [Salmonella enterica subsp. enterica sero... gi\|16764576, gi\|... - gi\|16764576\|ref\|NP_460191.1\| NAD-dependent deacetylase [Salmonella typhimurium LT2], gi\|16419739\|gb\|... gi\|194402841, gi... - gi\|194444178\|ref\|YP_002040476.1\| NAD-dependent deacetylase [Salmonella enterica subsp. enterica sero... lcl\|NC_016856.1_... - [gene=cobB] [protein=NAD-dependent deacetylase] [protein_id=YP_005236979.1] [location=1264938..12657... NPD_SALTI - NAD-dependent deacetylase OS=Salmonella typhi GN=npdA PE=3 SV=1 gi\|168467181, gi... - gi\|195630353\|gb\|EDX48979.1\| NAD-dependent deacetylase [Salmonella enterica subsp. enterica serovar N... gi\|197937808, gi... - gi\|198243292\|ref\|YP_002215916.1\| NAD-dependent deacetylase [Salmonella enterica subsp. enterica sero... gi\|197263070, gi... - gi\|197263070\|ref\|ZP_03163144.1\| NAD-dependent deacetylase [Salmonella enterica subsp. enterica serov... gi\|197248811, gi... - gi\|197248811\|ref\|YP_002146820.1\| NAD-dependent deacetylase [Salmonella enterica subsp. enterica sero... gi\|194735957, gi... - gi\|194735957\|ref\|YP_002114227.1\| NAD-dependent deacetylase [Salmonella enterica subsp. enterica sero... NPD_SALTY - NAD-dependent deacetylase OS=Salmonella typhimurium GN=cobB PE=3 SV=1 NPD_SALTI - NAD-dependent deacetylase OS=Salmonella typhi GN=cobB PE=3 SV=1 NPD_SALTY - NAD-dependent deacetylase OS=Salmonella typhimurium GN=npdA PE=3 SV=1 gi\|214002214 - gi\|214002214\|ref\|ZP_03412949.1\| NAD-dependent deacetylase [Salmonella enterica subsp. enterica serov... gi\|213864853 - gi\|213864853\|ref\|ZP_03386972.1\| NAD-dependent deacetylase [Salmonella enterica subsp. enterica serov... gi\|238910959 - gi\|238910959\|ref\|ZP_04654796.1\| NAD-dependent deacetylase [Salmonella enterica subsp. enterica serov...	315.0	[0..1]	[273..1]
gi\|82777267, gi\|... - gi\|82777267\|ref\|YP_403616.1\| NAD-dependent deacetylase [Shigella dysenteriae Sd197], gi\|81241415\|gb\|...	315.0	[0..1]	[273..1]
gi\|75175756, gi\|... - gi\|75175756\|ref\|ZP_00695956.1\| COG0846: NAD-dependent protein deacetylases, SIR2 family [Shigella bo...	314.0	[0..1]	[273..1]
gi\|224584272, gi... - gi\|224584272\|ref\|YP_002638070.1\| NAD-dependent deacetylase [Salmonella enterica subsp. enterica sero... gi\|62127374, gi\|... - gi\|62179741\|ref\|YP_216158.1\| NAD-dependent deacetylase [Salmonella enterica subsp. enterica serovar ...	314.0	[0..1]	[273..1]
gi\|18977526, gi\|... - gi\|18977526\|ref\|NP_578883.1\| NAD-dependent deacetylase [Pyrococcus furiosus DSM 3638], gi\|18893233\|g...	310.0	[0..30]	[271..49]
NPD_PYRFU - NAD-dependent deacetylase OS=Pyrococcus furiosus GN=npdA PE=3 SV=2 NPD_PYRFU - NAD-dependent protein deacylase OS=Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc...	309.0	[0..30]	[271..2]
gi\|238728942, gi... - gi\|77980020\|ref\|ZP_00835435.1\| COG0846: NAD-dependent protein deacetylases, SIR2 family [Yersinia in...	305.0	[0..4]	[270..2]

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Predicted Domain #1

Region A:
Residues: [1-273]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MLSRRGHRLS RFRKNKRRLR ERLRQRIFFR DKVVPEAMEK PRVLVLTGAG ISAESGIRTF  60
   61 RAADGLWEEH RVEDVATPEG FDRDPELVQA FYNARRRQLQ QPEIQPNAAH LALAKLQDAL 120
  121 GDRFLLVTQN IDNLHERAGN TNVIHMHGEL LKVRCSQSGQ VLDWTGDVTP EDKCHCCQFP 180
  181 APLRPHVVWF GEMPLGMDEI YMALSMADVF IAIGTSGHVY PAAGFVHEAK LHGAHTVELN 240
  241 LEPSQVGNEF AEKYYGPASQ VVPEFVEKLL EGL

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	80.154902
Match:	1s5pA
Description:	Structure and substrate binding properties of cobB, a Sir2 homolog protein deacetylase from Eschericia coli.
Matching Structure (courtesy of the PDB):

Predicted functions:

Term	Confidence	Notes
transcription regulator activity	2.31731368009317	bayes_pls_golite062009
DNA binding	1.84059392605809	bayes_pls_golite062009
NAD-dependent protein deacetylase activity	1.83565083706175	bayes_pls_golite062009
NAD-dependent histone deacetylase activity	1.83565083706175	bayes_pls_golite062009
nucleic acid binding	1.83132687449755	bayes_pls_golite062009
histone deacetylase activity	1.74695290583345	bayes_pls_golite062009
protein deacetylase activity	1.73884380618194	bayes_pls_golite062009
binding	1.63619372613603	bayes_pls_golite062009
transporter activity	1.02987325768951	bayes_pls_golite062009
transmembrane transporter activity	0.879539673228343	bayes_pls_golite062009
deacetylase activity	0.850785854706901	bayes_pls_golite062009
transcription factor activity	0.758967814548108	bayes_pls_golite062009
catalytic activity	0.739210399081789	bayes_pls_golite062009
transcription factor binding	0.64778523540991	bayes_pls_golite062009
substrate-specific transmembrane transporter activity	0.62029498163975	bayes_pls_golite062009
inorganic cation transmembrane transporter activity	0.56000396203236	bayes_pls_golite062009
monovalent inorganic cation transmembrane transporter activity	0.52020182886741	bayes_pls_golite062009
protein binding	0.475479132768057	bayes_pls_golite062009
hydrogen ion transmembrane transporter activity	0.47231237137431	bayes_pls_golite062009
substrate-specific transporter activity	0.128843577740998	bayes_pls_golite062009
transcription repressor activity	0.116839617002046	bayes_pls_golite062009
hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds	0.114062221123972	bayes_pls_golite062009
hydrolase activity	0.0875567934348688	bayes_pls_golite062009
transcription cofactor activity	0.05634462944063	bayes_pls_golite062009

TMHMM	2.0c	PSIPRED	v2.61
SignalP	3.0	COILS	1999
DISOPRED	v0.1	NCBI nr	06/2007
PSI-BLAST	2.2.18	FFAS	ffas03
PDB	06/2007	Pfam	22
HMMER	2.3.2

View Structure Prediction Details

Top Sequence Alignment Hits

Predicted functions: